New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library (...) !
BioRuby project
23 months
265
13
90103
6487
Parser of scientific names (...) !
Dmitry Mozzherin
6 days
18
5
48740
5263
1
9
Basic spreadsheet content extraction using apache poi (...)
Stuart Owen, Finn Bacall, Quyen Nguyen
6 weeks
6
2
41385
2840
0
13
Biogem is a software generator for Ruby in (...) !
Raoul J.P. Bonnal, Pjotr Prins
11 months
14
11
37997
3115
0
0
Binder of samtools for Ruby, on the top (...) !
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
8 weeks
19
6
37262
5827
Support for interacting with taverna 2 server (...) !
Robert Haines, Finn Bacall
8 weeks
2
...
29394
2170
The Ruby ucsc api: accessing the ucsc genome (...) !
Hiroyuki Mishima, Jan Aerts
13 months
13
1
24871
2350
Gadgets for bioinformatics (...)
Shintaro Katayama
22 months
1
24670
3348
Http requests to entrez e-utilities (...)
Jared Ning
5 days
4
...
23952
2197
3
3
A Ruby api for interacting with biomart services (...) !
Darren Oakley
3 years
17
5
22949
1386
0
0
Support for interacting with taverna 2 workflows (...) !
Finn Bacall, Robert Haines, David Withers et al.
13 months
22395
1393
Blast search made easy! (...) !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
5 weeks
70
43
22238
3581
0
157
Create pretty svg-format images of features, gene models (...)
Dan MacLean
15 months
9
5
20044
3994
Gff3 parser for big data (...) !
Pjotr Prins
2 years
6
2
18642
1363
Maf parser for BioRuby (...)
Clayton Wheeler
2 years
10
31
17897
1849
Interfaces with biomodel search engine (...) !
Niall Beard
3 years
1
...
15838
1108
0
0
A biogem to submit jobs on a queue (...)
Francesco Strozzi
2 years
5
...
15545
1637
Log4r wrapper with extra features for roles and (...) !
Pjotr Prins
3 years
4
2
14829
984
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer (...) !
Pjotr Prins
5 months
12
...
14645
1779
A simple obo file handler (...) !
mjy
3 years
4
...
13865
949
A fast parser for fastq files (...)
Francesco Strozzi
2 years
10
...
11160
994
Support for multiple sequence alignments (msa) (...)
Pjotr Prins
11 months
7
5
10963
1062
Swiss army knife of tabulated data; transforming/filtering tab/csv (...)
Pjotr Prins
11 months
8
20
10897
1234
0
0
An open source framework for transforming heterogeneous data (...)
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
3 months
12
2
10745
2035
Data mining algorithms for jRuby (...)
arrigonialberto86
19 months
14
3
9609
1495
A tool to classify and manipulate pfemp1 dbl-alpha (...)
George Githinji
2 years
1
...
9406
814
Pipeline to remove contaminations from est libraries (...)
Philipp Comans
3 years
2
1
9303
688
0
0
Low memory sequence emitters (...)
Pjotr Prins
11 months
8
1
8981
830
0
0
A nexus file format (phylogenetic inference) parser in (...) !
mjy
4 years
1
...
8841
537
A wrapper for the signal peptide prediction algorith (...)
Ben J Woodcroft
8 months
3
...
8441
869
0
0
Build genome output files (...)
Michael Barton
20 months
5
...
8366
505
0
0
Ruby support for the baclava file format (...) !
Robert Haines
14 months
1
...
8328
514
0
0
BioRuby assembly plugin (...) !
Chase Miller, Francesco Strozzi
4 years
4
...
8106
540
0
0
Simple morphbank (http://morphbank.net) services accessor (...) !
mjy
3 years
1
...
7947
463
0
0
A BioRuby plugin for interaction with the transmembrane (...)
Ben J. Woodcroft
2 years
2
...
7868
686
Lightweight Ruby api for ncbi eutils (...)
Joon Lee, aka seouri
22 months
8
...
7682
659
Tool to work with polyploids, ngs and molecular (...)
Ricardo H.  Ramirez-Gonzalez
7 weeks
2
1
7640
2961
0
21
A biogem for counting small kmers for fingerprinting (...)
Ben J Woodcroft
23 months
5
...
7627
797
BioRuby plugin for reading and writing nexml (http://nexml.org) (...) !
Rutger Vos, Anurag Priyam
2 years
7
2
7625
570
Ruby wrapper for sambamba tool (...)
Artem Tarasov
2 years
2
...
7525
670
0
0
A BioRuby plugin for calculating the isoelectric point (...)
George Githinji, Pascal Betz
3 years
3
...
7437
572
This is a development release (...) !
Pjotr Prins and Trevor Wennblom
5 years
7422
610
Supports linking of models within a ror application (...) !
Stuart Owen, Quyen Nguyen
2.2
13 months
...
7421
502
0
0
Library for visualizing genomic regions (...) !
Jan Aerts
1.4
7 years
22
1
6895
426
A BioRuby plugin: handling genomic interavals and overlaps (...)
Hiroyuki Mishima
4 years
4
...
6792
499
Bio-ngs provides a framework for handling ngs data (...)
Francesco Strozzi, Raoul J.P. Bonnal
2 years
30
14
6562
518
Running and parsing of the protein transmembrane domain (...)
Ben J Woodcroft
3 years
1
...
6181
408
Reading/writing bgzf blocks (...)
Artem Tarasov, Clayton Wheeler
2 years
2
...
5881
663
0
0
Basespace Ruby sdk is a Ruby based software (...)
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
20 months
11
2
5556
878
Ruby binding for bwa mapping software (...) !
Francesco Strozzi
4 years
4
...
5502
415
0
0
Gene ontology (go) interface for Ruby (...)
Ben J Woodcroft
4 years
10
...
5393
398
A plugin that allows you to parse large (...)
robsyme
3 years
1
...
5285
415
0
0
Read and manipulate cd-hit clusters (...)
George Githinji
2 years
2
1
5093
554
Iterate through a samtools pileup file (...)
Ben J. Woodcroft
2 years
2
...
5093
428
Taverna player is a rails plugin to run (...)
Robert Haines
8 weeks
4
3
4916
1042
0
6
Api to ensembl databases (...) !
Jan Aerts, Francesco Strozzi
4 years
38
5
4896
223
Ruby binding for samtools tabix (...)
throwern
19 months
3
...
4813
535
Ruby wrapper for the gff3-pltools (...)
Marjan Povolni
2 years
4267
409
Parser to work with file formats used in (...)
Ben J Woodcroft
3 months
...
4242
1182
Chembl rest api client, parser and container (...)
Mitsuteru Nakao
2 years
1
1
4213
412
Next-generation mapping of mutations (...)
Dan MacLean
2 years
2
...
4192
415
Ruby binding to the ucsc kent utilities (...)
throwern
2 years
2
...
4183
415
Fast multi-threaded vcf parser (...)
Pjotr Prins
4 months
16
7
4160
1222
0
22
Geneexpression illuminahumanannotation (...)
Raoul J.P. Bonnal
4 years
1
...
4140
277
Implementation of the plasmoap algorithm (...)
Ben J Woodcroft
3 years
1
...
4107
282
0
0
Bioinformatics triple-store support (...)
Pjotr Prins
2 years
4
1
3887
297
Parse affymetrix cel/cdf files (...)
Pjotr Prins
3 years
2
1
3853
314
0
0
Timeseries modules for statsample (...)
Ankur Goel, Claudio Bustos
19 months
3585
525
BioRuby core plugins, most and stable plugins. blastxmlparser, (...) !
Raoul J.P. Bonnal
3 years
1
...
3580
272
Server for polymarker. to be used with cron (...)
Ricardo H.  Ramirez-Gonzalez
7 weeks
...
3455
1411
Programmatic interface to the cnls nuclear localisation signal (...)
Ben J. Woodcroft
2 years
1
...
3413
272
BioRuby plugin for unichem rest web service (...)
Mitsuteru Nakao
2 years
3397
402
Enables the localisation predictor wolf psort to be (...)
Ben J Woodcroft
3 years
1
...
3361
283
Reports whether a nucleotide change results in synonymous (...)
Dan MacLean
23 months
...
3300
426
This biogem is built around krona, a flashy (...)
Ben J. Woodcroft
20 months
1
...
3289
418
Parse pfam hmm definition files (...)
Ben J. Woodcroft
2 years
1
...
3030
284
0
0
A protparam compatible utility for BioRuby (...)
hryk
2 years
1
...
2964
274
Bio-gag is a biogem for detecting and correcting (...)
Ben J Woodcroft
2 years
2
...
2862
272
Publish scientific results to the semantic web (...) !
Will Strinz
10 months
3
16
2683
407
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover) (...)
Andrei Rozanski
13 months
1
...
2449
545
Rocker (...)
Luis (Coto) Orellana, Luis M. Rodriguez-R
3 months
2448
2345
Bindings to some internals of the velvet assembler (...)
Ben Woodcroft
3 months
1
2161
786
BioRuby plugin for sun grid engine (...) !
Toshiaki Katayama
4 years
4
...
2136
124
0
0
Hello world plugin for the BioRuby (just for (...)
Toshiaki Katayama
4 years
3
...
2136
145
0
0
Digests dna based on restriction enzyme cut patterns (...) !
Trevor Wennblom
3 years
1
2129
140
0
0
Does high pairwise alignment of sequencing reads with (...)
John T. Prince
5 years
1
...
2047
124
Rubybhl is a simple request/response wrapper for the (...) !
Matt Yoder
14 months
6
...
2005
159
0
0
Gggenome Ruby client (...)
Mitsuteru Nakao
20 months
1
...
1882
268
0
0
Pass a full citation, get the bibtex back, (...) !
Matt Yoder
5 months
1
1879
821
0
0
A method to get the nucleotide sequence of (...)
Ben J Woodcroft
4 years
1
...
1876
142
A general purpose framework for scripted handling of (...) development/stable
mjy
2 years
2
1
1850
296
14
14
BioRuby core ext: plugins which require external library (...) !
Raoul J.P. Bonnal, Pjotr Prins
3 years
1
...
1850
128
Restriction enzyme dataset (...) !
Sir Richard J. Roberts, Trevor Wennblom
3 years
...
1840
138
Meta package for biolinux distribution (...) !
Raoul J.P. Bonnal
3 years
2
...
1830
135
Biological extensions for the intermine webservice client library (...) !
Alex Kalderimis
3 years
1
...
1830
443
0
0
A Ruby api to the ensembl database (...) !
Jan Aerts, Francesco Strozzi
3 years
3
...
1814
142
0
0
Biostars data-mining and statistical analysis (...)
Joachim Baran
12 months
1808
432
One-line summary of your gem (...)
Toshiaki Katayama
3 years
1
...
1801
135
Ruby ensembl rest api (...)
Alberto Donizetti
19 months
3
...
1798
269
0
2
Decoding the dbsnp bitfield (...)
Hiroyuki Mishima
3 years
4
...
1788
136
0
0
Phyloxml plugin for BioRuby (...)
Diana Jaunzeikare, Clayton Wheeler
2 years
3
...
1760
134
Wrapper around the exportpred algorithm for predicting p (...)
Ben J Woodcroft
3 years
1
...
1755
150
Generalized linear models for statsample (...)
Ankur Goel
19 months
1750
276
A simple biogem that allows computation of the (...)
Ben J Woodcroft
3 years
1
...
1724
132
Hydropathy scale for BioRuby (...)
Ben J Woodcroft
3 years
1
...
1716
139
0
0
Enables parsing of hmmer version 3 reports (...)
Christian Zmasek, Ben J Woodcroft
2 years
1
1
1630
146
Build graph with jRuby (...)
Matteo Picciolini
2 years
1529
139
A programmatic interface to the ipcress in-silico pcr (...)
Ben J Woodcroft
2 years
3
...
1522
138
Dead simple method of running shell commands from (...)
Ben J. Woodcroft
15 months
...
1497
279
0
0
Interface for express beta diversity (...)
Ben J. Woodcroft
15 months
...
1484
285
Bio-repeatmasker (...)
Andrei Rozanski
15 months
1455
270
Client for xoopit's cloudquery api (...)
Cameron Walters, nb.io
5 years
5
...
1407
395
A parser for cigar format alignments (...)
Ben J Woodcroft
14 months
4
...
1341
299
0
0
Reads metadata from integrated microbial genomes (img) metadata (...)
Ben J. Woodcroft
2 years
...
1275
142
Web server for bio-samtools (...)
homonecloco
11 months
...
1191
296
Parse stockholm sequence alignment format (...)
Ben J. Woodcroft
22 months
2
...
1063
145
Ruby wrapper to run standard-raxml for maximum likelihood (...)
Fernando Izquierdo
21 months
...
996
139
Fast storage and comparison of chr+pos(+alt) locations (...)
Pjotr Prins
6 months
981
298
Csshttprequest is cross-domain ajax using css as a (...)
Cameron Walters, Randy Reddig
6 years
89
1
712
200
0
0
Mine publications for gene names (...)
Pjotr Prins
14 months
...
672
144
0
0
A sequence read archive (sra) download script and (...)
Ben J. Woodcroft
4 months
1
...
670
329
A restful service for sharing genomic data (...) !
Joachim Baran, Robert Buels, Michel Dumontier
13 months
596
167
Helper methods for reading .delta files (...)
robsyme
4 weeks
...
556
556
Ruby inferface for kseq.h by heng li for (...)
Fedor Gusev
9 months
1
...
520
147
A Ruby wrapper on the open tree api (...) beta
Matt Yoder
7 months
...
480
182
Tools to work with fasta files, indexed with (...)
homonecloco
6 months
...
442
155
0
0
Tools to manipulate blat files from the command (...)
homonecloco
6 months
...
428
152
0
0
(...) pre
pre
414
31
Faldo location output method for bio::location in BioRuby (...)
Joachim Baran, Naohisa Goto
5 months
...
383
156
0
0
Emulates as if old BioRuby biofetch alives (...)
Naohisa Goto
5 months
...
381
156
0
0
Csshttprequest is cross-domain ajax using css (...)
Cameron Walters, Randy Reddig
0.1
6 years
368
100
!
Bioinformatics. aggregate fastqc (quality control for next generation (...) new
Raoul Jean Pierre Bonnal
5 weeks
...
185
185
!
A pipeline manager (...) new
Francesco Strozzi
4 weeks
8
10
169
169
(...) pre
pre
163
38
*) gem downloads (total & last 90 days) from rubygems.org as of 2015-04-28
**) number of commits on GitHub (last 7 days & last 90 days)